chr4-23707992-T-C

Variant names:

• chr4-23707992-T-C
• rs10938957
• ENST00000514290.1:n.118-60327T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514290.1(ENSG00000250137):​n.118-60327T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,054 control chromosomes in the GnomAD database, including 13,464 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (13464 hom., cov: 32)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 3 publications found

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250137	ENST00000514290.1	n.118-60327T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61254 AN: 151936 Hom.: 13466 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.429

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.403 AC: 61260 AN: 152054 Hom.: 13464 Cov.: 32 AF XY: 0.400 AC XY: 29698 AN XY: 74332

African (AFR) AF: 0.240 AC: 9974 AN: 41488

American (AMR) AF: 0.415 AC: 6341 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5166

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4965 AN: 10550

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33904 AN: 67968

Other (OTH) AF: 0.427 AC: 900 AN: 2106

Alfa AF: 0.425 Hom.: 5870

Bravo AF: 0.394

Asia WGS AF: 0.301 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.77
DANN	Benign	0.57
PhyloP100		-0.0070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10938957; hg19: chr4-23709615;